radis.io.exomolapi module

API for Exomol molecular database

Borrowed from the Exojax code (which you should also have a look at !), by @HajimeKawahara, under MIT License.

check_bdat(bdat)[source]

cheking codes in .broad Args:

bdat: exomol .broad data given by exomolapi.read_broad

Returns:

code level: None, a0, a1, other codes unavailable currently,

make_j2b(bdat, alpha_ref_default=0.07, n_Texp_default=0.5, jlower_max=None)[source]

compute j2b (code a0, map from jlower to alpha_ref)

Args:

bdat: exomol .broad data given by exomolapi.read_broad alpha_ref_default: default value n_Texp_default: default value jlower_max: maximum number of jlower

Returns:

j2alpha_ref[jlower] provides alpha_ref for jlower j2n_Texp[jlower] provides nT_exp for jlower

make_jj2b(bdat, j2alpha_ref_def, j2n_Texp_def, jupper_max=None)[source]

compute jj2b (code a1, map from (jlower, jupper) to alpha_ref and n_Texp)

Args:

bdat: exomol .broad data given by exomolapi.read_broad j2alpha_ref_def: default value from a0 j2n_Texp_def: default value from a0 jupper_max: maximum number of jupper

Returns:

jj2alpha_ref[jlower,jupper] provides alpha_ref for (jlower, jupper) jj2n_Texp[jlower,jupper] provides nT_exp for (jlower, jupper)

Note:

The pair of (jlower, jupper) for which broadening parameters are not given, jj2XXX contains None.

pickup_gE(states, trans, trans_file, dic_def, trans_lines=False, skip_optional_data=True)[source]

extract g_upper (gup), E_lower (elower), and J_lower and J_upper from states DataFrame and insert them into the transition DataFrame.

Parameters

  • states (states DataFrame - the i, E, g, J are in the 4 first columns)

  • trans (transition numpy array)

  • trans_file (name of the transition file)

  • trans_lines (By default (False) we use nu_lines computed using the state file, i.e. E_upper - E_lower. If trans_nuline=True, we use the nu_lines in the transition file. Note that some trans files do not this info.)

  • dic_def (Informations about additional quantum labels)

  • add_quantum_labels (bool . If True fetch all quantum labels in dic_def[‘quantum_labels’] from states into transitions)

Return type

A, nu_lines, elower, gup, jlower, jupper, mask, **quantum_labels

Notes

We first convert pandas DataFrame to ndarray. The state counting numbers in states DataFrame is used as indices of the new array for states (newstates). We remove the state count numbers as the column of newstate, i.e. newstates[:,k] k=0: E, 1: g, 2: J. Then, we can directly use the state counting numbers as mask.

States by default has columns

#       i      E             g    J    v
0       1      0.0           1    0    0
1       2      1.448467      3    1    0
2       3      4.345384      5    2    0
3       4      8.690712      7    3    0
read_broad(broadf)[source]

Reading braodening file (.broad) :Parameters: broadf (.broad file)

Return type

broadening info in bdat form (pandas), defined by this instance.

Notes

See Table 16 in https://arxiv.org/pdf/1603.05890.pdf

read_def(deff)[source]

Exomol IO for a definition file

Parameters

deff (definition file)

Returns

  • n_Texp (float) – temperature exponent

  • alpha_ref (float) – broadening parameter

  • molmass (float) – molecular mass

  • numinf (List[float]) – limit points ([w(0), w(1), ..., w(n)], n+1 elements) defining the spectral ranges appearing in the name of *.trans.bz2 files (["w(0)-w(1)", "w(1)-w(2)", ..., w(n-1)-w(n)], n elements)

  • numtag (List[str]) – tag for wavelength ranges.

  • Note – For some molecules, ExoMol provides multiple trans files. numinf and numtag are the ranges and identifiers for the multiple trans files.

read_pf(pff)[source]

Exomol IO for partition file

Note:

T=temperature QT=partition function

Args:

pff: partition file

Returns:

partition data in pandas DataFrame

read_states(statesf, dic_def, engine='vaex', skip_optional_data=True)[source]

Exomol IO for a state file

Notes

States f format

i=state counting number
E=state energy
g=state degeneracy
J=total angular momentum

See Table 11 in https://arxiv.org/pdf/1603.05890.pdf

Parameters

  • statesf (str) – state file

  • dic_def (dict) – Info from def file to read extra quantum numbers

  • engine (str) – parsing engine to use (‘vaex’, ‘csv’)

  • skip_optional_data (bool) – If False, fetch all fields which are marked as available in the ExoMol definition file. If True, load only the first 4 columns of the states file (“i”, “E”, “g”, “J”). The structure of the columns above 5 depend on the the definitions file (*.def) and the Exomol version. If skip_optional_data=False, two errors may occur:

Returns

  • states data in pandas DataFrame

  • If 'vaex', also writes a local hdf5 file statesf.with_suffix('.hdf5')

References

1

Tennyson, J., Yurchenko, S. N., Al-Refaie, A. F., Barton, E. J., Chubb, K. L., Coles, P. A., … Zak, E. (2016). The ExoMol database: molecular line lists for exoplanet and other hot atmospheres. https://doi.org/10.1016/j.jms.2016.05.002

2

Tennyson, J., Yurchenko, S. N., Al-Refaie, A. F., Clark, V. H. J., Chubb, K. L., Conway, E. K., … Yurchenko, O. P. (2020). The 2020 release of the ExoMol database: Molecular line lists for exoplanet and other hot atmospheres. Journal of Quantitative Spectroscopy and Radiative Transfer, 255, 107228. https://doi.org/10.1016/j.jqsrt.2020.107228

read_trans(transf, engine='vaex')[source]

Exomol IO for a transition file

Notes

Transf format

i_upper=Upper state counting number
i_lower=Lower state counting number
A=Einstein coefficient in s-1
nu_lines=transition wavenumber in cm-1

See Table 12 in https://arxiv.org/pdf/1603.05890.pdf [Exomol-2016]

Parameters

  • transf (transition file)

  • engine (parsing engine to use (‘vaex’, ‘csv’))

Return type

transition data in vaex/pandas DataFrame